FMO DATABASE

FMODB ID: 2NM7R

Calculation Name: 2F9D-P-Xray372

Preferred Name: Splicing factor 3B subunit 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2F9D

Chain ID: P

ChEMBL ID: CHEMBL1229013

UniProt ID: O75533

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	39
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-151767.037141
FMO2-HF: Nuclear repulsion	134754.825205
FMO2-HF: Total energy	-17012.211935
FMO2-MP2: Total energy	-17060.81777

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(P:377:SER)

Summations of interaction energy for fragment #1(P:377:SER)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-2.549	-0.727	-0.009	-0.89	-0.923	0.004

Interaction energy analysis for fragmet #1(P:377:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : 0.005

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	P	379	THR	0	0.029	-0.010	3.722	-2.654	-0.832	-0.009	-0.890	-0.923	0.004
4	P	380	PRO	0	0.022	-0.010	6.054	0.884	0.884	0.000	0.000	0.000	0.000
5	P	381	GLU	-1	-0.827	-0.887	8.353	-2.049	-2.049	0.000	0.000	0.000	0.000
6	P	382	GLN	0	0.036	0.018	5.462	-0.886	-0.886	0.000	0.000	0.000	0.000
7	P	383	LEU	0	0.002	-0.004	4.940	0.582	0.582	0.000	0.000	0.000	0.000
8	P	384	GLN	0	0.018	0.025	8.544	0.377	0.377	0.000	0.000	0.000	0.000
9	P	385	ALA	0	-0.012	0.002	11.650	0.169	0.169	0.000	0.000	0.000	0.000
10	P	386	TRP	0	0.025	0.012	9.640	0.165	0.165	0.000	0.000	0.000	0.000
11	P	387	ARG	1	0.915	0.940	9.305	0.754	0.754	0.000	0.000	0.000	0.000
12	P	388	TRP	0	0.001	0.001	13.857	0.050	0.050	0.000	0.000	0.000	0.000
13	P	389	GLU	-1	-0.952	-0.979	14.071	-0.081	-0.081	0.000	0.000	0.000	0.000
14	P	390	ARG	1	0.815	0.891	13.337	-0.062	-0.062	0.000	0.000	0.000	0.000
15	P	391	GLU	-1	-0.907	-0.935	17.065	-0.143	-0.143	0.000	0.000	0.000	0.000
16	P	392	ILE	0	-0.012	-0.028	19.470	0.013	0.013	0.000	0.000	0.000	0.000
17	P	393	ASP	-1	-0.823	-0.881	18.240	0.103	0.103	0.000	0.000	0.000	0.000
18	P	394	GLU	-1	-0.901	-0.942	21.493	0.080	0.080	0.000	0.000	0.000	0.000
19	P	395	ARG	1	0.811	0.891	23.457	0.106	0.106	0.000	0.000	0.000	0.000
20	P	396	ASN	0	-0.064	-0.025	24.682	-0.013	-0.013	0.000	0.000	0.000	0.000
21	P	397	ARG	1	0.761	0.865	25.596	-0.041	-0.041	0.000	0.000	0.000	0.000
22	P	398	PRO	0	-0.052	-0.027	26.941	-0.008	-0.008	0.000	0.000	0.000	0.000
23	P	399	LEU	0	0.010	0.009	30.337	0.006	0.006	0.000	0.000	0.000	0.000
24	P	400	SER	0	-0.008	0.003	33.210	-0.002	-0.002	0.000	0.000	0.000	0.000
25	P	401	ASP	-1	-0.854	-0.955	36.143	0.031	0.031	0.000	0.000	0.000	0.000
26	P	402	GLU	-1	-0.980	-0.973	38.506	0.047	0.047	0.000	0.000	0.000	0.000
27	P	403	GLU	-1	-0.812	-0.892	32.202	0.034	0.034	0.000	0.000	0.000	0.000
28	P	404	LEU	0	-0.027	-0.018	36.825	-0.007	-0.007	0.000	0.000	0.000	0.000
29	P	405	ASP	-1	-0.908	-0.963	38.558	0.012	0.012	0.000	0.000	0.000	0.000
30	P	406	ALA	0	-0.063	-0.019	39.172	-0.004	-0.004	0.000	0.000	0.000	0.000
31	P	407	MET	0	-0.085	-0.033	35.446	-0.003	-0.003	0.000	0.000	0.000	0.000
32	P	408	PHE	0	-0.058	-0.026	39.748	-0.008	-0.008	0.000	0.000	0.000	0.000
33	P	409	PRO	0	-0.030	0.003	43.349	0.002	0.002	0.000	0.000	0.000	0.000
34	P	410	GLU	-1	-0.909	-0.974	46.491	-0.001	-0.001	0.000	0.000	0.000	0.000
35	P	411	GLY	0	-0.041	-0.020	49.958	-0.003	-0.003	0.000	0.000	0.000	0.000
36	P	412	TYR	0	-0.004	0.004	47.724	-0.004	-0.004	0.000	0.000	0.000	0.000
37	P	413	LYS	1	0.886	0.949	49.910	0.006	0.006	0.000	0.000	0.000	0.000
38	P	414	VAL	0	0.082	0.043	45.359	-0.003	-0.003	0.000	0.000	0.000	0.000
39	P	415	LEU	0	-0.018	-0.010	47.056	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(P:377:SER)